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Joshi AG, Harini K, Meenakshi I, Shafi KM, Pasha SN, Mahita J, Sajeevan RS, Karpe SD, Ghosh P, Nitish S, Gandhimathi A, Mathew OK, Prasanna SH, Malini M, Mutt E, Naika M, Ravooru N, Rao RM, Shingate PN, Sukhwal A, Sunitha MS, Upadhyay AK, Vinekar RS, Sowdhamini R. A knowledge-driven protocol for prediction of proteins of interest with an emphasis on biosynthetic pathways. MethodsX 2020; 7:101053. [PMID: 33024710 PMCID: PMC7528181 DOI: 10.1016/j.mex.2020.101053] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 08/29/2020] [Indexed: 11/28/2022] Open
Abstract
This protocol describes a stepwise process to identify proteins of interest from a query proteome derived from NGS data. We implemented this protocol on Moringa oleifera transcriptome to identify proteins involved in secondary metabolite and vitamin biosynthesis and ion transport. This knowledge-driven protocol identifies proteins using an integrated approach involving sensitive sequence search and evolutionary relationships. We make use of functionally important residues (FIR) specific for the query protein family identified through its homologous sequences and literature. We screen protein hits based on the clustering with true homologues through phylogenetic tree reconstruction complemented with the FIR mapping. The protocol was validated for the protein hits through qRT-PCR and transcriptome quantification. Our protocol demonstrated a higher specificity as compared to other methods, particularly in distinguishing cross-family hits. This protocol was effective in transcriptome data analysis of M. oleifera as described in Pasha et al.Knowledge-driven protocol to identify secondary metabolite synthesizing protein in a highly specific manner. Use of functionally important residues for screening of true hits. Beneficial for metabolite pathway reconstruction in any (species, metagenomics) NGS data.
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Affiliation(s)
- Adwait G Joshi
- National Centre for Biological Sciences (NCBS-TIFR), GKVK campus, Bellary road, Bangalor 560065, Karnataka, India
| | - K Harini
- National Centre for Biological Sciences (NCBS-TIFR), GKVK campus, Bellary road, Bangalor 560065, Karnataka, India
| | - Iyer Meenakshi
- National Centre for Biological Sciences (NCBS-TIFR), GKVK campus, Bellary road, Bangalor 560065, Karnataka, India
| | - K Mohamed Shafi
- National Centre for Biological Sciences (NCBS-TIFR), GKVK campus, Bellary road, Bangalor 560065, Karnataka, India.,The University of Trans-Disciplinary Health Sciences and Technology (TDU), Yelahanka, Bangalore 560064, Karnataka, India
| | - Shaik Naseer Pasha
- National Centre for Biological Sciences (NCBS-TIFR), GKVK campus, Bellary road, Bangalor 560065, Karnataka, India
| | - Jarjapu Mahita
- National Centre for Biological Sciences (NCBS-TIFR), GKVK campus, Bellary road, Bangalor 560065, Karnataka, India
| | - Radha Sivarajan Sajeevan
- National Centre for Biological Sciences (NCBS-TIFR), GKVK campus, Bellary road, Bangalor 560065, Karnataka, India
| | - Snehal D Karpe
- National Centre for Biological Sciences (NCBS-TIFR), GKVK campus, Bellary road, Bangalor 560065, Karnataka, India
| | - Pritha Ghosh
- National Centre for Biological Sciences (NCBS-TIFR), GKVK campus, Bellary road, Bangalor 560065, Karnataka, India
| | - Sathyanarayanan Nitish
- National Centre for Biological Sciences (NCBS-TIFR), GKVK campus, Bellary road, Bangalor 560065, Karnataka, India.,The University of Trans-Disciplinary Health Sciences and Technology (TDU), Yelahanka, Bangalore 560064, Karnataka, India
| | - A Gandhimathi
- National Centre for Biological Sciences (NCBS-TIFR), GKVK campus, Bellary road, Bangalor 560065, Karnataka, India
| | - Oommen K Mathew
- National Centre for Biological Sciences (NCBS-TIFR), GKVK campus, Bellary road, Bangalor 560065, Karnataka, India
| | - Subramanian Hari Prasanna
- National Centre for Biological Sciences (NCBS-TIFR), GKVK campus, Bellary road, Bangalor 560065, Karnataka, India
| | - Manoharan Malini
- National Centre for Biological Sciences (NCBS-TIFR), GKVK campus, Bellary road, Bangalor 560065, Karnataka, India
| | - Eshita Mutt
- National Centre for Biological Sciences (NCBS-TIFR), GKVK campus, Bellary road, Bangalor 560065, Karnataka, India
| | - Mahantesha Naika
- National Centre for Biological Sciences (NCBS-TIFR), GKVK campus, Bellary road, Bangalor 560065, Karnataka, India
| | - Nithin Ravooru
- National Centre for Biological Sciences (NCBS-TIFR), GKVK campus, Bellary road, Bangalor 560065, Karnataka, India
| | - Rajas M Rao
- National Centre for Biological Sciences (NCBS-TIFR), GKVK campus, Bellary road, Bangalor 560065, Karnataka, India
| | - Prashant N Shingate
- National Centre for Biological Sciences (NCBS-TIFR), GKVK campus, Bellary road, Bangalor 560065, Karnataka, India
| | - Anshul Sukhwal
- National Centre for Biological Sciences (NCBS-TIFR), GKVK campus, Bellary road, Bangalor 560065, Karnataka, India
| | - Margaret S Sunitha
- National Centre for Biological Sciences (NCBS-TIFR), GKVK campus, Bellary road, Bangalor 560065, Karnataka, India
| | - Atul K Upadhyay
- National Centre for Biological Sciences (NCBS-TIFR), GKVK campus, Bellary road, Bangalor 560065, Karnataka, India.,Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala 147004, Punjab, India
| | - Rithvik S Vinekar
- National Centre for Biological Sciences (NCBS-TIFR), GKVK campus, Bellary road, Bangalor 560065, Karnataka, India
| | - Ramanathan Sowdhamini
- National Centre for Biological Sciences (NCBS-TIFR), GKVK campus, Bellary road, Bangalor 560065, Karnataka, India
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Upadhyay AK, Chacko AR, Gandhimathi A, Ghosh P, Harini K, Joseph AP, Joshi AG, Karpe SD, Kaushik S, Kuravadi N, Lingu CS, Mahita J, Malarini R, Malhotra S, Malini M, Mathew OK, Mutt E, Naika M, Nitish S, Pasha SN, Raghavender US, Rajamani A, Shilpa S, Shingate PN, Singh HR, Sukhwal A, Sunitha MS, Sumathi M, Ramaswamy S, Gowda M, Sowdhamini R. Genome sequencing of herb Tulsi (Ocimum tenuiflorum) unravels key genes behind its strong medicinal properties. BMC Plant Biol 2015; 15:212. [PMID: 26315624 PMCID: PMC4552454 DOI: 10.1186/s12870-015-0562-x] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 06/24/2015] [Indexed: 05/21/2023]
Abstract
BACKGROUND Krishna Tulsi, a member of Lamiaceae family, is a herb well known for its spiritual, religious and medicinal importance in India. The common name of this plant is 'Tulsi' (or 'Tulasi' or 'Thulasi') and is considered sacred by Hindus. We present the draft genome of Ocimum tenuiflurum L (subtype Krishna Tulsi) in this report. The paired-end and mate-pair sequence libraries were generated for the whole genome sequenced with the Illumina Hiseq 1000, resulting in an assembled genome of 374 Mb, with a genome coverage of 61 % (612 Mb estimated genome size). We have also studied transcriptomes (RNA-Seq) of two subtypes of O. tenuiflorum, Krishna and Rama Tulsi and report the relative expression of genes in both the varieties. RESULTS The pathways leading to the production of medicinally-important specialized metabolites have been studied in detail, in relation to similar pathways in Arabidopsis thaliana and other plants. Expression levels of anthocyanin biosynthesis-related genes in leaf samples of Krishna Tulsi were observed to be relatively high, explaining the purple colouration of Krishna Tulsi leaves. The expression of six important genes identified from genome data were validated by performing q-RT-PCR in different tissues of five different species, which shows the high extent of urosolic acid-producing genes in young leaves of the Rama subtype. In addition, the presence of eugenol and ursolic acid, implied as potential drugs in the cure of many diseases including cancer was confirmed using mass spectrometry. CONCLUSIONS The availability of the whole genome of O.tenuiflorum and our sequence analysis suggests that small amino acid changes at the functional sites of genes involved in metabolite synthesis pathways confer special medicinal properties to this herb.
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Affiliation(s)
- Atul K Upadhyay
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bellary Road, 560 065, Bangalore, India.
| | - Anita R Chacko
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bellary Road, 560 065, Bangalore, India.
| | - A Gandhimathi
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bellary Road, 560 065, Bangalore, India.
| | - Pritha Ghosh
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bellary Road, 560 065, Bangalore, India.
| | - K Harini
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bellary Road, 560 065, Bangalore, India.
| | - Agnel P Joseph
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bellary Road, 560 065, Bangalore, India.
| | - Adwait G Joshi
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bellary Road, 560 065, Bangalore, India.
- Manipal University, Madhav Nagar, 576104, Manipal, Karnataka, India.
| | - Snehal D Karpe
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bellary Road, 560 065, Bangalore, India.
| | - Swati Kaushik
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bellary Road, 560 065, Bangalore, India.
| | - Nagesh Kuravadi
- Centre for Cellular and Molecular Platforms, GKVK Campus, Bellary Road, 560 065, Bangalore, India.
| | - Chandana S Lingu
- Centre for Cellular and Molecular Platforms, GKVK Campus, Bellary Road, 560 065, Bangalore, India.
| | - J Mahita
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bellary Road, 560 065, Bangalore, India.
| | - Ramya Malarini
- Centre for Cellular and Molecular Platforms, GKVK Campus, Bellary Road, 560 065, Bangalore, India.
| | - Sony Malhotra
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bellary Road, 560 065, Bangalore, India.
| | - Manoharan Malini
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bellary Road, 560 065, Bangalore, India.
| | - Oommen K Mathew
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bellary Road, 560 065, Bangalore, India.
- School of Chemical and Biotechnology, SASTRA (A University), 613401, Thanjavur, TamilNadu, India.
| | - Eshita Mutt
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bellary Road, 560 065, Bangalore, India.
| | - Mahantesha Naika
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bellary Road, 560 065, Bangalore, India.
| | - Sathyanarayanan Nitish
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bellary Road, 560 065, Bangalore, India.
| | - Shaik Naseer Pasha
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bellary Road, 560 065, Bangalore, India.
- Manipal University, Madhav Nagar, 576104, Manipal, Karnataka, India.
| | - Upadhyayula S Raghavender
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bellary Road, 560 065, Bangalore, India.
| | - Anantharamanan Rajamani
- Centre for Cellular and Molecular Platforms, GKVK Campus, Bellary Road, 560 065, Bangalore, India.
| | - S Shilpa
- Centre for Cellular and Molecular Platforms, GKVK Campus, Bellary Road, 560 065, Bangalore, India.
| | - Prashant N Shingate
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bellary Road, 560 065, Bangalore, India.
- Manipal University, Madhav Nagar, 576104, Manipal, Karnataka, India.
| | | | - Anshul Sukhwal
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bellary Road, 560 065, Bangalore, India.
- School of Chemical and Biotechnology, SASTRA (A University), 613401, Thanjavur, TamilNadu, India.
| | - Margaret S Sunitha
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bellary Road, 560 065, Bangalore, India.
| | - Manojkumar Sumathi
- Centre for Cellular and Molecular Platforms, GKVK Campus, Bellary Road, 560 065, Bangalore, India.
| | - S Ramaswamy
- Centre for Cellular and Molecular Platforms, GKVK Campus, Bellary Road, 560 065, Bangalore, India.
| | - Malali Gowda
- Centre for Cellular and Molecular Platforms, GKVK Campus, Bellary Road, 560 065, Bangalore, India.
| | - Ramanathan Sowdhamini
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bellary Road, 560 065, Bangalore, India.
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